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Sample GSM989761 Query DataSets for GSM989761
Status Public on Aug 23, 2012
Title PC 452N
Sample type RNA
 
Channel 1
Source name reference RNA
Organism Homo sapiens
Characteristics reference: common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PC 452N2
Organism Homo sapiens
Characteristics individual: PC 452N
disease state: Normal
tissue: prostate
Growth protocol All prostate samples used for this study were collected at the Stanford University Medical Center between 1999 and 2007 with patient's informed consent under an Institutional Review Board (IRB)-approved protocol. Multiple tissue samples were harvested from each prostate, flash-frozen and stored at 80oC. Frozen sections of each prostate sample were performed and evaluated by a genitourinary pathologist (JKM). The tumor and nontumor areas were marked and contaminating tissues were trimmed away from the block as described previously.48 Tumor samples in which at least 90% of the epithelial cells were cancerous were selected for extraction of DNA and RNA. In total, we selected 98 tumors from 86 patients that met these criteria. Associated clinical data were collected and included preoperative PSA levels, clinical stage, pathological stage, tumor Gleason grade and clinical follow-up. Recurrence was defined as a measurable serum PSA (>0.1ng/ml on two consecutive measurements) after surgery.
Gene-expression profiling was performed as reported. Briefly, Cy5-labeled cDNA was prepared by using 50ug of total RNA from prostate samples and Cy3-labeled cDNA was prepared by using common reference mRNA (Stratagene-Agilent Technologies, Inc, Santa Clara, CA, USA), pooled from 11 established human cell lines. For each experimental sample, Cy5- and Cy3-labeled samples were cohybridized to HEEBO spotted microarrays.49 HEEBO microarrays were manufactured in the Stanford Functional Genomics Facility at Stanford University and contained 44-544 70-mer probes.
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol After hybridization, microarrays were imaged using an Axon GenePix 4000 scanner (Axon Instruments-Molecular Devices, LLC, Sunnyvale, CA, USA). Fluorescence ratios for array elements were extracted using GENEPIX software and uploaded into the Stanford Microarray Database for subsequent analysis.
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-08/81195.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 21, 2012
Last update date Aug 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9497
Series (1)
GSE40272 Gene-expression profiling of prostate tumors

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 4964 5525 39 52 4925 5472 5483 5667 40 54 5444 5614 0 0 2216 2794 7 21 100 100 100 100 10397 11058 .9 1.111 1.031 1.003 1.098 2.349 52 286 1.138 .96 80 1660 6180 6 14 30 38 0 4391 41 4348 .883 4503 4461 1.133 .819 -.18 -.287
2 3280 3762 39 60 3241 3702 2893 3807 40 65 2854 3746 0 0 2340 2584 7 28 100 100 98 100 6943 6600 .875 1.142 1.313 1.47 1.055 3.746 52 245 1.115 .96 80 1810 6190 7 15 45 53 0 2990 48 2942 .908 3025 2977 1.102 1.043 -.14 .061
3 6958 12573 41 67 6917 12505 8342 15379 41 75 8301 15311 0 0 2985 5888 7 40 100 100 100 100 19422 23612 .553 1.808 1.844 1.625 1.808 2.083 52 277 1.846 .98 90 1960 6180 5 14 59 68 0 9991 53 9937 1.437 12221 12167 .696 1.466 .523 .552
4 5206 5907 43 70 5162 5837 5506 6165 50 83 5462 6094 0 0 1440 1742 40 98 100 100 100 100 10999 11556 .884 1.131 1.116 1.078 1.107 2.005 32 212 1.146 .95 70 2100 6180 6 13 74 81 0 4694 56 4639 .899 4899 4843 1.113 .887 -.154 -.174
5 275 153 44 82 230 71 300 152 53 94 255 70 0 0 104 60 41 92 92 30 86 3 301 325 3.239 .309 .275 .315 .308 3.569 52 230 .311 .53 80 2260 6180 6 14 90 98 0 122 65 56 .245 121 56 4.076 .218 -2.027 -2.197
6 3717 6066 56 101 3661 5964 3861 6408 65 110 3805 6306 0 0 908 1431 27 59 100 100 100 100 9625 10111 .614 1.629 1.657 1.635 1.614 1.806 52 274 1.633 .98 90 2410 6180 5 14 104 113 0 4821 80 4739 1.295 5092 5011 .772 1.317 .372 .397
7 150 134 41 70 109 64 155 131 44 77 114 60 0 0 20 50 13 34 100 65 100 43 173 174 1.703 .587 .526 .455 .622 3.545 32 226 .758 .61 70 2560 6180 6 13 120 127 0 106 56 51 .467 104 48 2.143 .418 -1.1 -1.258
8 6886 13181 39 73 6847 13107 7690 14651 40 82 7651 14577 0 0 1905 3821 6 39 100 100 100 100 19954 22228 .522 1.914 1.905 1.875 1.884 1.977 52 253 1.936 .97 80 2720 6180 6 14 136 144 0 10475 58 10416 1.521 11643 11584 .657 1.514 .605 .598
9 73 110 39 67 33 42 73 110 41 77 33 42 0 0 11 39 10 44 96 50 84 18 75 75 .786 1.273 1.273 1.19 1.512 3.796 32 159 4.027 .45 60 2860 6180 7 13 151 157 0 87 53 33 1.011 87 33 .989 1.011 .016 .016
10 69 108 38 64 31 44 75 102 41 76 36 38 0 0 27 47 13 58 61 40 52 5 75 74 .705 1.419 1.056 1.538 1.653 4.245 80 255 3.591 .56 100 3010 6180 5 15 164 174 -50 86 51 35 1.128 81 30 .887 .839 .174 -.254
11 141 349 37 65 104 283 145 353 39 73 107 288 0 0 40 128 7 44 100 96 98 90 387 395 .367 2.721 2.692 2.575 2.642 2.318 52 212 3.199 .86 80 3170 6180 6 14 181 189 0 277 52 225 2.162 281 229 .462 2.139 1.113 1.097
12 152 906 37 60 114 846 159 969 39 67 121 909 0 0 46 343 9 32 96 96 94 96 960 1030 .135 7.421 7.512 7.064 7.606 2.581 52 212 7.781 .95 80 3320 6180 6 14 196 204 0 720 48 672 5.897 770 722 .17 5.97 2.56 2.578
13 125 179 37 69 88 110 131 163 39 75 93 94 0 0 31 77 6 38 100 90 98 61 198 187 .8 1.25 1.011 1.149 1.146 2.508 52 230 2.003 .7 80 3470 6180 6 14 211 219 0 142 55 87 .993 130 75 1.007 .803 -.01 -.316
14 123 194 38 69 84 125 121 181 42 92 83 112 0 0 15 63 32 162 100 15 87 0 209 195 .672 1.488 1.349 1.282 1.595 2.644 32 211 2.43 .67 70 3630 6180 6 13 227 234 0 154 55 99 1.183 144 89 .846 1.072 .242 .101
15 45 58 38 63 6 -4 45 53 41 73 6 -9 0 0 7 29 25 91 1 0 0 0 2 -3 null null null 3.689 3.816 4.895 80 320 38.577 .09 100 3770 6170 4 14 240 250 -50 46 50 -3 null 42 -7 null null null null
16 637 1068 37 66 600 1002 668 1112 39 72 630 1046 0 0 159 291 5 30 100 100 100 100 1602 1676 .599 1.67 1.66 1.67 1.701 1.886 52 217 1.695 .96 80 3930 6180 6 14 257 265 0 849 52 796 1.327 884 831 .754 1.319 .408 .4
17 64 119 37 63 26 56 64 117 39 71 26 54 0 0 11 44 5 29 96 67 88 44 82 80 .464 2.154 2.077 1.897 2.01 3.284 52 191 4.854 .55 80 4080 6180 6 14 272 280 0 95 50 45 1.712 93 43 .584 1.65 .775 .723
18 44 63 38 61 5 1 42 52 39 72 4 -9 0 0 7 52 7 46 31 6 15 2 6 -5 5 .2 null 3.343 4.733 5.136 80 236 12.78 .44 100 4220 6170 4 14 285 295 -50 50 48 1 .159 41 -7 6.292 null -2.653 null
19 132 206 38 67 93 138 139 208 41 82 100 140 0 0 86 120 10 75 86 71 76 41 231 240 .674 1.484 1.4 1.592 1.469 3.351 80 284 2.032 .75 100 4380 6180 5 15 301 311 0 164 53 110 1.179 165 111 .848 1.113 .238 .154
20 542 3279 38 61 504 3217 604 3604 39 72 565 3542 0 0 181 1047 8 45 100 100 100 100 3721 4107 .157 6.383 6.269 6.716 6.316 2.224 52 203 6.466 .97 80 4530 6180 6 14 317 325 0 2606 48 2556 5.072 2864 2815 .197 4.982 2.343 2.317

Total number of rows: 44544

Table truncated, full table size 9199 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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